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Lysinibacillus boronitolerans MSR1, a bacterium isolated from yogurt, was characterized through a detailed genomic and phylogenetic analysis. The strain demonstrated the ability to grow in MRS broth at pH 5-8 and exhibited positive activity in citrate utilization, catalase, oxidase, Methyl Red-Voges Proskauer (MR-VP), and Triple Sugar Iron (TSI) tests while being negative for amylase degradation and sulfide production. Whole-genome sequencing and Average Nucleotide Identity (ANI) analysis revealed a close genetic relationship between MSR1 and previously reported L. boronitolerans strains, with ANI values ranging from 95.25% to 98.30%, particularly for L. boronitolerans strain NBRC103108. Phylogenetic analyses based on whole-genome and 16S rRNA sequences confirmed the taxonomic placement of MSR1 within the L. boronitolerans species. A circular genome comparison highlighted the presence of unique genomic regions in MSR1, notably around the 3500 kbp mark, indicating the acquisition of novel genes that may contribute to its distinct phenotypic traits. Antibiotic susceptibility testing revealed a high level of resistance in MSR1 to glycopeptides and aminoglycosides, while the strain remained susceptible to imipenem, with in silico analysis identifying key antimicrobial resistance (AMR) genes, including qacJ, vanW, vanT, and FosBx1, which confer resistance to disinfectants, vancomycin, and fosfomycin through efflux pumps and target modification mechanisms. Five distinct biosynthetic gene cluster (BGC) regions were identified in the MSR1 genome, encoding genes for lanthipeptide-class-iii, RiPP-like, T3PKS, beta-lactone, terpene, and NRPS-like clusters. Pan-genome analysis suggested that L. boronitolerans possesses an open pan-genome, with a substantial proportion of accessory and unique genes. Functional annotation of core, accessory, and unique genes revealed that core genes are predominantly associated with metabolic processes, while accessory and unique genes are involved in information processing, storage, and defence mechanisms. These findings enhance our understanding of the genomic diversity, evolutionary dynamics, and potential adaptive strategies of L. boronitolerans MSR1, providing new insights into its ecological and functional roles.

Long-distance extracellular electron transfer has been observed in Gram-negative bacteria and plays roles in both natural and engineering processes. The electron transfer can be mediated by conductive protein appendages (in short unicellular bacteria such as Geobacter species) or by conductive cell envelopes (in filamentous multicellular cable bacteria). Here we show that Lysinibacillus varians GY32, a filamentous unicellular Gram-positive bacterium, is capable of bidirectional extracellular electron transfer. In microbial fuel cells, L. varians can form centimetre-range conductive cellular networks and, when grown on graphite electrodes, the cells can reach a remarkable length of 1.08 mm. Atomic force microscopy and microelectrode analyses suggest that the conductivity is linked to pili-like protein appendages. Our results show that long-distance electron transfer is not limited to Gram-negative bacteria. Long-distance extracellular electron transfer has been observed in Gram-negative bacteria. Here, Yang et al. show that a filamentous, unicellular Gram-positive bacterium is capable of bidirectional extracellular electron transfer, and forms centimetre-range conductive networks consisting of 1mm-long cells and conductive appendages.

The present study investigated biosorption of Pb (II) and Zn (II) using a heavy metal tolerant bacterium Oceanobacillus profundus KBZ 3-2 isolated from a contaminated site. The effects of process parameters such as effect on bacterial growth, pH and initial lead ion concentration were studied. The results showed that the maximum removal percentage for Pb (II) was 97% at an initial concentration of 50 mg/L whereas maximum removal percentage for Zn (II) was at 54% at an initial concentration of 2 mg/L obtained at pH 6 and 30 °C. The isolated bacteria were found to sequester both Pb (II) and Zn (II) in the extracellular polymeric substance (EPS). The EPS facilitates ion exchange and metal chelation-complexation by virtue of the existence of ionizable functional groups such as carboxyl, sulfate, and phosphate present in the protein and polysaccharides. Therefore, the use of indigenous bacteria in the remediation of contaminated water is an eco-friendly way of solving anthropogenic contamination.

This study isolated a novel thermophilic heterotrophic nitrifying bacterium, Aeribacillus pallidus sp. GW-E, from aerobic composting. Under conditions of 55 °C, the utilization efficiency of NH₄⁺-N, NO₃⁻-N, and NO₂⁻-N were 87.42%, 21.44%, and 51.68%, respectively. Whole-genome analysis identified key nitrogen metabolism genes ( amt , npd , nirA , gdhA , glnA , and gltBD ) as well as heat stress-related genes ( GRPE , hslO , groES , groEL ). Response surface optimization revealed that under conditions of a C/N ratio of 15, a temperature of 54 °C, and a pH of 8, the NH₄⁺-N utilization efficiency reached 100%. Enzyme activity assays indicated that the activities of three enzymes in the ammonia assimilation pathway were GS 1.014 ± 0.030 U/mg, GDH 1.114 ± 0.090 U/mg, and GOGAT 11.611 ± 0.061 U/mg, which were significantly higher than those of other pathways ( P  < 0.05). Nitrogen balance analysis confirmed that approximately 40.04% of the nitrogen was assimilated. In conclusion, the bacterium primarily utilizes ammonia assimilation, with additional assimilated nitrate reduction and nitrification pathways for nitrogen transformation. This strain represents a valuable microbial resource and provides a theoretical basis for nitrogen retention in high-temperature composting systems.

Soluble phosphorus scarcity severely limits plant growth and crop yield. In this study, a strain of inorganic phosphorus-solubilizing bacteria, Lysinibacillus sphaericus , was isolated from rice rhizosphere soil. The available phosphorus content in liquid inorganic phosphorus identification medium and in L. sphaericus -inoculated soil increased from 204.28 mg/L to 1124.68 mg/L and from 4.75 mg/kg to 7.04 mg/kg, respectively. The pH decreased significantly from 6.87 to 6.14. Incubation with L. sphaericus significantly increased malic and succinic acid content in the liquid inorganic phosphorus identification medium and increased acid phosphatase and alkaline phosphatase activity in the soil. Inoculation with L. sphaericus significantly increased rice growth, chlorophyll a/b content, and photosynthesis by increasing the soluble phosphorus content in the rice rhizosphere soil under phosphorus-deficient conditions. Further analysis revealed that L. sphaericus improved soil phosphorus release by decreasing soil pH and promoting acid phosphatase and alkaline phosphatase activity. This study supports the production of microbial fertilizers to improve rice yield in phosphorus-deficient conditions.

Species of Anoxybacillus are widespread in geothermal springs, manure, and milk-processing plants. The genus is composed of 22 species and two subspecies, but the relationship between its lifestyle and genome is little understood. In this study, two high-quality draft genomes were generated from Anoxybacillus spp. SK3-4 and DT3-1, isolated from Malaysian hot springs. De novo assembly and annotation were performed, followed by comparative genome analysis with the complete genome of Anoxybacillus flavithermus WK1 and two additional draft genomes, of A. flavithermus TNO-09.006 and A. kamchatkensis G10. The genomes of Anoxybacillus spp. are among the smaller of the family Bacillaceae. Despite having smaller genomes, their essential genes related to lifestyle adaptations at elevated temperature, extreme pH, and protection against ultraviolet are complete. Due to the presence of various competence proteins, Anoxybacillus spp. SK3-4 and DT3-1 are able to take up foreign DNA fragments, and some of these transferred genes are important for the survival of the cells. The analysis of intact putative prophage genomes shows that they are highly diversified. Based on the genome analysis using SEED, many of the annotated sequences are involved in carbohydrate metabolism. The presence of glycosyl hydrolases among the Anoxybacillus spp. was compared, and the potential applications of these unexplored enzymes are suggested here. This is the first study that compares Anoxybacillus genomes from the aspect of lifestyle adaptations, the capacity for horizontal gene transfer, and carbohydrate metabolism.

A novel bacterium, designated as strain M3 T , was isolated from a hyperalkaline spring in the Philippines and identified as a new species within the genus Lysinibacillus through 16 S rRNA gene sequence and genomic analyses. Although strain M3 T shared a high 16 S rRNA gene sequence similarity (> 98.7%) with many Lysinibacillus species, the digital DNA-DNA hybridization and orthologous average nucleotide identity values between strain M3 T and its closet relative, Lysinibacillus xylanilyticus DSM 23,493 T , were 41.2% and 90.6%, respectively—both below the established threshold for prokaryotic species delineation. Genome mining of the 5.3 Mbp-draft genome of strain M3 T revealed eight biosynthetic gene clusters, which shared little sequence similarity with characterized clusters, suggesting the potential for encoding novel specialized metabolites. The cells of strain M3 T were Gram-stain-positive, aerobic, rod-shaped, non-motile, and capable of endospore formation. Optimum growth was observed at 30 °C, pH 8.0, and 0.5% (w/v) NaCl. The major respiratory quinone was menaquinone-7, and the predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and two unknown phospholipids. Its fatty acid profile showed an elevated level of iso-C 15:0 , and the peptidoglycan type was determined to be A4 α (L-Lys–D-Asp). This study contributes to the growing database and understanding of the genus and aims to help drive future research on the bioactive potential of the genus. Lysinibacillus zambalensis sp. nov. is proposed with strain M3 T as the type strain (= TISTR 10640 T  = BIOTECH 10973 T ).

A Gram-stain-positive aerobic, rod-shaped, spore-producing bacterium forming colonies with convex elevation and a smooth, intact margin was isolated from a freshwater sample collected from a well situated in an agricultural field. The 16S rRNA gene sequence of the isolated strain BA0131T showed the highest sequence similarity to Lysinibacillus yapensis ylb-03T (99.25%) followed by Ureibacillus chungkukjangi 2RL3-2T (98.91%) and U. sinduriensis BLB-1T (98.65%). The strain BA0131T was oxidase and catalase positive and urease negative. It also tested positive for esculin hydrolysis and reduction of potassium nitrate, unlike its phylogenetically closest relatives. The predominant fatty acids in strain BA0131T included were anteiso-C15:0, iso-C16:0, iso-C15:0, iso-C14:0 and the major polar lipids comprised were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The respiratory quinones identified in strain BA0131T were MK8 (H2) (major) and MK8 (minor). The strain BA0131T shared the lowest dDDH values with L. yapensis ylb-03T (21%) followed by U. chungkukjangi 2RL3-2T (24.2%) and U. sinduriensis BLB-1T (26.4%) suggesting a closer genetic relationship U. sinduriensis BLB-1T. The ANI percentage supported the close relatedness with U. sinduriensis BLB-1T (83.61%) followed by U. chungkukjangi 2RL3-2T (82.03%) and U. yapensis ylb-03T (79.57%). The core genome-based phylogeny constructed using over 13,704 amino acid positions and 92 core genes revealed the distinct phylogenetic position of strain BA0131T among the genus Ureibacillus. The distinct physiological, biochemical characteristics and genotypic relatedness data indicate the strain BA0131T represents a novel species of the genus Ureibacillus for which the name Ureibacillus aquaedulcis sp. nov. (Type strain, BA0131T = MCC 5284T = JCM 36475T) is proposed. Additionally, based on extensive genomic and phylogenetic analyses, we propose reclassification of two species, L. yapensis and L. antri, as U. yapensis comb. nov. (Type strain, ylb-03T = JCM 32871T = MCCC 1A12698T) and U. antri (Type strain, SYSU K30002T = CGMCC 1.13504T = KCTC 33955T).

An endospore producing, strict aerobic, Gram-stain-positive, orange-colored colony forming bacterium designated as strain JC1013 T was isolated from an orange pond near a solar saltern of Tamil Nadu, India. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain was affiliated to the family Bacillaceae of the phylum Firmicutes . Strain showed highest 16S rRNA gene sequence identity of 98.7% with Mesobacillus selenatarsenatis SF-1  T and below 98.3% with other members of the genus Mesobacillus . Strain JC1013 T produced carotenoid pigments and indole compounds. Major cellular fatty acids of strain JC1013 T were iso-C 15:0, anteiso-C 15:0 , C 16:0 3-OH, iso-C 17:0 ω10c and summed feature 4 (iso-C 17:1 I/ anteisoB). Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids and four unidentified phospholipids. Strain JC1013 T constituted m -diaminopimelic acid as diagnostic cell wall amino acids. MK-7 is the predominant menaquinone of strain JC1013 T . The genome size of strain JC1013 T was 4.6 Mbp and its G + C content was 42.7 mol%. For the affirmation of strain’s taxonomic status, a detailed phylogenomic study was done. Based on the phylogenetic analyses, low ANI (84.6%), AAI (88.5%) values, in-silico DDH (< 29%) value, morphological, physiological and chemo-taxonomical characteristics, strain JC1013 T was clearly distinguished from the nearest phylogenetic neighbor, Mesobacillus selenatarsenatis SF-1 T to conclude that it is a new species of the genus Mesobacillus . We propose the name as Mesobacillus aurantius with type strain JC1013 T (= NBRC 114146 T  = KACC 21451  T ).

A Gram-stain positive, long-rod-shaped, motile, and aerobic bacterial strain, designated 16A2E T , was isolated from mangrove sediment sample. The 16S rRNA gene sequence similarity analysis indicated that strain 16A2E T exhibited high similarity to Ornithinibacillus contaminans CCUG 53201 T (98.2%), Ornithinibacillus bavariensis WSBC 24001 T (98.1%), and Ornithinibacillus scapharcae TW25 T (97.7%). Strain 16A2E T grew within a temperature range of 20–50 °C (optimum 40 °C), a pH range of 6.0–9.0 (optimum pH 8.0), and in the presence of 0–10% (w/v) NaCl (optimum 1%). The genome size of strain 16A2E T is 3.60 Mbp, with a G + C content of 36.7%. The overall genome related index (OGRI) analyses revealed low average nucleotide identity (ANI < 75.9%), average amino acid identity (AAI < 77.5%), and digital DNA-DNA hybridization (dDDH < 19.8%) with other species in the genus Ornithinibacillus . Chemotaxonomic analyses revealed that the major polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phospholipids, and an aminophospholipid. The predominant fatty acids were iso-C 15:0 , anteiso-C 15:0 , and anteiso-C 17:0 . The sole respiratory quinone was menaquinone-7 (MK-7), and the peptidoglycan amino acid type was determined to be A4β. Based on phenotypic and genotypic analyses, strain 16A2E T (= GDMCC 1.4379 T  = JCM 36753 T ) represents a novel species within the genus Ornithinibacillus , for which the name Ornithinibacillus xuwenensis sp. nov. is proposed.